October 17, 2012

The tangled web of humanity

Indian populations are composed of two ancestral components: Ancestral North Indians (ANI) and Ancestral South Indians (ASI), discovered by Reich et al. (2009). In that paper, it was also shown that ASI forms a clade with East Eurasians, while ANI does so with West Eurasians.

Patterson et al. (2012) published a different pattern: non-Sardinian Europeans have North Eurasian-like ancestry that links them to Amerindian populations. It is thus possible that ASI and the East Eurasian-like admixture in North Europeans may share a common evolutionary history:

Now, consider a hypothetical population of the Indian Cline. A European population is related to it both via its ANI/West Eurasian ancestry, but also via its ASI ancestry, because the East_Eurasian component in Europeans shares a portion of ancestry (indicated by the red arrow) with ASI.

Sardinians lack (or have less of) this "red arrow" portion of ancestry.

It is also possible that ANI itself may have some East_Eurasian ancestry, like Europeans do; this is not indicated in the figure. More on this later.

Consider the following D-statistic:

D(European, Sardinian, Indian, San)

As we shall see, this takes positive values, consistent with the idea of gene flow between Europeans and Indians at the exclusion of Sardinians. However, this gene flow may involve either the West Eurasian component in the ancestry of Indians (i.e., this component is more related to Europeans than to Sardinians), or to the ASI component (which is related to Europeans via the common "red arrow" portions of ancestry).

We can figure out what is going on by trying different Indian populations along the Indian Cline, and seeing whether the D-statistic is inflated/deflated in populations of greater ANI/ASI ancestry.

For each Indian Cline population, I list the ANI percentage, as estimated by Reich et al. (2009) in the last column, and the D-statistic of the above given form for different pairs of Indian and European populations.

We can plot the D-statistic vs. ANI for each of our European populations:

The correlation coefficients confirm the visual impression, that for the HGDP Russians there is a significantly negative relationship between ANI admixture in an Indian Cline population and the D-statistic:

Russian Orcadian French Lithuanians

-0.8631118 0.08670188 0.1870127 -0.1889908

In other words, the evidence for gene flow between Russians and Indians is maximized when south Indian (ASI-rich) populations are used.

The lack of a clear pattern in the other three populations is itself interesting. One possible explanation involves East Eurasian-like admixture in the ANI, a conjecture which would make sense, given that all non-Sardinian continental West Eurasians seem to possess it.

If that is true, then as we go "south" along the Indian Cline, ASI related admixture inflates the D-statistic by increasing the "red arrow" overlap with the East Eurasian-like admixture in Europeans. As we go "north" along this cline, then the D-statistic decreases, due to ASI-reduction, but also increases, due to East Eurasian-like admixture in ANI, with an end result of no clear pattern in the superposition of processes.

In any case, this is an interesting example of a crisscrossing type of admixture where unrelated processes (east Eurasian-like admixture in Russians and ASI admixture in Indians) combine to present an unusual effect.

As I previously stated somewhere else. What I believe is that the ancestral "North Eurasian" genes are nothing more than just a Northern shifted version of an "Gedrosia" (proto West Asian?) like component. I believe that the East Eurasian similarities in ancestral North Europeans is not admixture but some common ancient affinities. As we all know the East Eurasian affinities are not exclusive to North Europeans but also find in the West Asian component and just lacking or noisy in Sardinian like populations.

I believe that the East Eurasian similarities in ancestral North Europeans is not admixture but some common ancient affinities.

The evidence for admixture with the f3 statistic is pretty conclusive evidence for admixture. That statistic does not take negative values for tree topologies that do not involve admixture, so anyway one reshuffles populations to establish "ancient common affinities", he cannot come up with a negative f3.

The open question is what were the mixing elements that are represented by Sardinians and Asians/Amerindians today.

What I believe is that the ancestral "North Eurasian" genes are nothing more than just a Northern shifted version of an "Gedrosia" (proto West Asian?) like component. I believe that the East Eurasian similarities in ancestral North Europeans is not admixture but some common ancient affinities.

That it is due to admixture, and not common descent, with an East Eurasian-like population is beyond doubt. The test results are very robust on that point. There are just some questions about its timing.

As we all know the East Eurasian affinities are not exclusive to North Europeans but also find in the West Asian component and just lacking or noisy in Sardinian like populations.

West Asians have much less ancient East Eurasian admixture than northern Europeans (whether western or eastern).

I'll take a crack at this. The number is basically the sum over all BABA -ABBA (normalized with all counts), where A vs. B stands for a specific SNP variant that was typed for (and thus may contain biases). In D(European, Sardinian, Indian, San), San is the outside reference, and you are testing whether "European" is closer to Indian where Indian has a particular SNP different from the outside reference (i.e., BABA counts), or Sardinian is closer (ABBA counts). If D is positive and significant, then (sum over all) BABA > ABBA. Of course, one has to be careful that an admixture with the outside reference is not what creates the BABA counts.

The four numbers in your question are simply the four results of the D-statistic for the four different "European" populations listed.

@Onur"West Asians have much less ancient East Eurasian admixture than northern Europeans (whether western or eastern)."

Dienekes and you are probably right that North Europeans have some more ancient East Eurasian admixture but much is exaggerated and I think its rather some additional East Eurasian admixture to that found in Proto West Asian (Gedrosia like). So I believe North European = Gedrosia + slight additional Siberian/Amerindian.

Dienekes and you are probably right that North Europeans have some more ancient East Eurasian admixture but much is exaggerated and I think its rather some additional East Eurasian admixture to that found in Proto West Asian (Gedrosia like). So I believe North European = Gedrosia + slight additional Siberian/Amerindian.

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